MAST - Motif Alignment and Search Tool
MAST version 3.0 (Release date: 2001/03/01 11:41:04)
For further information on how to interpret these results or to get
a copy of the MAST software please access http://meme.sdsc.edu.
REFERENCE
If you use this program in your research, please cite:
Timothy L. Bailey and Michael Gribskov,
"Combining evidence using p-values: application to sequence homology
searches", Bioinformatics, 14(48-54), 1998.
DATABASE AND MOTIFS
DATABASE lipocalin.s (peptide)
Last updated on Thu Mar 1 08:28:42 2001
Database contains 5 sequences, 903 residues
MOTIFS meme.lipocalin.zoops.4.sunsparcsolaris.html (peptide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 26 GACPAVRPMRNFDIQKFAGTWHEIAK
2 20 NNVFWILDTDYKNYLIQYMC
3 23 YDPDKKGHQDHVWILSRSKVLEG
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1 2
----- ----- -----
2 0.25
3 0.20 0.15
No overly similar pairs (correlation > 0.60) found.
Random model letter frequencies (from non-redundant database):
A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058
L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064
W 0.013 Y 0.033
SECTION I: HIGH-SCORING SEQUENCES
- Each of the following 5 sequences has E-value less than 10.
- The E-value of a sequence is the expected number of sequences
in a random database of the same size that would match the motifs as
well as the sequence does and is equal to the combined p-value of the
sequence times the number of sequences in the database.
- The combined p-value of a sequence measures the strength of the
match of the sequence to all the motifs and is calculated by
- finding the score of the single best match of each motif
to the sequence (best matches may overlap),
- calculating the sequence p-value of each score,
- forming the product of the p-values,
- taking the p-value of the product.
- The sequence p-value of a score is defined as the
probability of a random sequence of the same length containing
some match with as good or better a score.
- The score for the match of a position in a sequence to a motif
is computed by by summing the appropriate entry from each column of
the position-dependent scoring matrix that represents the motif.
- Sequences shorter than one or more of the motifs are skipped.
- The table is sorted by increasing E-value.
| Links | Sequence Name | Description | E-value | Length
|
|---|
|
| BBP_PIEBR
|
| 6.4e-59
| 173
|
|
| ICYA_MANSE
|
| 2.1e-58
| 189
|
|
| RETB_BOVIN
|
| 1.5e-27
| 183
|
|
| LACB_BOVIN
|
| 2.3e-23
| 178
|
|
| MUP2_MOUSE
|
| 4.5e-23
| 180
|
SECTION II: MOTIF DIAGRAMS
- The ordering and spacing of all non-overlapping motif occurrences
are shown for each high-scoring sequence listed in Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001.
- The POSITION p-value of a match is the probability of
a single random subsequence of the length of the motif
scoring at least as well as the observed match.
- For each sequence, all motif occurrences are shown unless there
are overlaps. In that case, a motif occurrence is shown only if its
p-value is less than the product of the p-values of the other
(lower-numbered) motif occurrences that it overlaps.
- The table also shows the E-value of each sequence.
- Spacers and motif occurences are indicated by
- occurrence of motif `n' with p-value less than 0.0001.
- Sequences longer than 1000 are not shown to scale and are indicated by thicker lines.
| Links | Name | Expect |    Motifs
|
|---|
|
| BBP_PIEBR
| 6.4e-59
|
|
|
| ICYA_MANSE
| 2.1e-58
|
|
|
| RETB_BOVIN
| 1.5e-27
|
|
|
| LACB_BOVIN
| 2.3e-23
|
|
|
| MUP2_MOUSE
| 4.5e-23
|
|
| SCALE
|
| |
| |
| |
| |
| |
| |
| |
| |
| 1
| 25
| 50
| 75
| 100
| 125
| 150
| 175
| |
|
|---|
SECTION III: ANNOTATED SEQUENCES
- The positions and p-values of the non-overlapping motif occurrences
are shown above the actual sequence for each of the high-scoring
sequences from Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001 as
defined in Section II.
- For each sequence, the first line specifies the name of the sequence.
- The second (and possibly more) lines give a description of the
sequence.
- Following the description line(s) is a line giving the length,
combined p-value, and E-value of the sequence as defined in Section I.
- The next line reproduces the motif diagram from Section II.
- The entire sequence is printed on the following lines.
- Motif occurrences are indicated directly above their positions in the
sequence on lines showing
- the motif number of the occurrence,
- the position p-value of the occurrence,
- the best possible match to the motif, and
- columns whose match to the motif has a positive score (indicated
by a plus sign).
BBP_PIEBR
LENGTH = 173 COMBINED P-VALUE = 1.28e-59 E-VALUE = 6.4e-59
DIAGRAM: 5-[1]-64-[2]-1-[3]-34
[1]
1.5e-24
GACPAVRPMRNFDIQKFAGTWHEIAK
++++++++++++++++++++++++++
1 NVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYP
[2] [3]
1.2e-19 1.8e-27
NNVFWILDTDYKNYLIQYMC YDPDKKGHQDHVWILSRSKVLEG
++++++++++++++++++++ +++++++++++++++++++++++
76 VGDSKIGKIYHKLTYGGVTKENVFNVLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLI
ICYA_MANSE
LENGTH = 189 COMBINED P-VALUE = 4.14e-59 E-VALUE = 2.1e-58
DIAGRAM: 6-[1]-67-[2]-1-[3]-46
[1]
3.0e-24
GACPAVRPMRNFDIQKFAGTWHEIAK
++++++++++++++++++++++++++
1 GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYKYDGKKASVYNSFVSNGVKEYMEGDLE
[2] [3]
4.6e-20 6.1e-27
NNVFWILDTDYKNYLIQYMC YDPDKKGHQDHVWILSRSKVLEG
+ ++++++++++++++++++ +++++++++++++++++++++++
76 IAPDAKYTKQGKYVMTFKFGQRVVNLVPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEGNTKEVVD
RETB_BOVIN
LENGTH = 183 COMBINED P-VALUE = 2.90e-28 E-VALUE = 1.5e-27
DIAGRAM: 3-[1]-71-[2]-63
[1]
2.5e-19
GACPAVRPMRNFDIQKFAGTWHEIAK
+++++++++++++ ++++++++++++
1 ERDCRVSSFRVKENFDKARFAGTWYAMAKKDPEGLFLQDNIVAEFSVDENGHMSATAKGRVRLLNNWDVCADMVG
[2]
3.7e-17
NNVFWILDTDYKNYLIQYMC
+ ++++++++++++++++++
76 TFTDTEDPAKFKMKYWGVASFLQKGNDDHWIIDTDYETFAVQYSCRLLNLDGTCADSYSFVFARDPSGFSPEVQK
LACB_BOVIN
LENGTH = 178 COMBINED P-VALUE = 4.54e-24 E-VALUE = 2.3e-23
DIAGRAM: 14-[1]-64-[2]-54
[1]
3.1e-18
GACPAVRPMRNFDIQKFAGTWHEIAK
+++++++++++ ++++++++++++++
1 MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQ
[2]
1.5e-13
NNVFWILDTDYKNYLIQYMC
++++ +++++++ ++++++
76 KWENGECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALE
MUP2_MOUSE
LENGTH = 180 COMBINED P-VALUE = 8.92e-24 E-VALUE = 4.5e-23
DIAGRAM: 16-[1]-62-[2]-56
[1]
8.4e-17
GACPAVRPMRNFDIQKFAGTWHEIAK
++++++++++++ +++++++++++++
1 MKMLLLLCLGLTLVCVHAEEASSTGRNFNVEKINGEWHTIILASDKREKIEDNGNFRLFLEQIHVLEKSLVLKFH
[2]
1.1e-14
NNVFWILDTDYKNYLIQYMC
+++++++++++++++++++
76 TVRDEECSELSMVADKTEKAGEYSVTYDGFNTFTIPKTDYDNFLMAHLINEKDGETFQLMGLYGREPDLSSDIKE
Debugging Information
CPU: nbcr2
Time 0.290000 secs.
mast meme.lipocalin.zoops.4.sunsparcsolaris.html -stdout
Button Help
Links to Entrez database at NCBI
Links to sequence scores (section I)
Links to motif diagrams (section II)
Links to sequence/motif annotated alignments (section III)
This information